BY Jennifer C. Pizer

August 06 2014 7:15 AM ET

The U.S. Supreme Court closed out its 2013-2014 term with Burwell v. Hobby Lobby, a decision whose repercussions already are being felt and promise to echo for years to come. By a 5-4 vote, the court held that religiously minded business owners essentially may “line-item veto” birth control coverage out of their employees’ health plans. Many wonder if the ruling means the court’s conservative majority has succeeded in elevating religious interests over equality in the marketplace. As the dust settles and immediate punditry has come and gone, I think we must answer yes, religion has won out over women’s reproductive freedom. And, some changes in the legal doctrine are problematic for everyone.

But, for LGBT equality, the answer is no — religion has not prevailed generally over civil rights. And this will remain so if we continue making the case for equality and collaborating within a broad, inclusive movement against the use of religion to discriminate. You’ll find a more detailed look at the ins and outs of the Hobby Lobby decision here: What the Supreme Court’s Hobby Lobby Decision Means for LGBT People.

As I explain in that post, in time, Hobby Lobby could stand for either of at least two propositions. It could mean that religious interests of those engaged in business should be accommodated if and only if there is no harm to others. That has been the rule in religious freedom cases for decades.

On the other hand, it could mean religious interests now trump other interests in many circumstances, with believers entitled to impose their views at others’ expense in ways rejected in the past. We flagged a range of potential problems for LGBT people and people living with HIV in our Hobby Lobby amicus brief, and Justice Ginsburg called out some of them in her passionate dissenting opinion.

Recent events suggest that an alarming push for religion to trump is already under way. In two cases brought by business owners objecting to all birth control services (Gilardi v. HHS and Autocam Corp. v. Burwell), the Supreme Court just ordered the appellate courts to reconsider owners’ arguments that the courts had rejected. In a third case, Wheaton College v. Burwell, the court granted temporary relief to one of the dozens of religiously affiliated employers objecting even to using the Health and Human Services form to be excused from providing contraception coverage. In a scathing dissent joined by both of the other women on the court, Justice Sotomayor said:

"I have deep respect for religious faith, for the important and selfless work performed by religious organizations, and for the values of pluralism protected by [the Religious Freedom Restoration Act] and the Free Exercise Clause. But the Court’s [order] in this case allows Wheaton’s beliefs … to trump the democratic interest in allowing the Government to enforce the law. … Our jurisprudence has over the years drawn a careful boundary between majoritarian democracy and the right of every American to practice his or her religion freely. We should not use [this rare form of court order] to work so fundamental a shift in that boundary."

The day after Hobby Lobby, conservative religious leaders petitioned President Obama to include a broad exemption in his imminent executive order forbidding discrimination against LGBT workers by federal contractors. Three weeks later, the executive order did not include an LGBT-specific religious carve-out. But what many in the LGBT community have not known is that religious organizations already have permission to discriminate against LGBT workers on federally funded projects thanks to President George W. Bush. President Obama’s new executive order does not change that, although a coalition of progressive religious and civil rights groups are pressing the administration to make such a change.

The Hobby Lobby decision emphasizes that it does not authorize employment discrimination. And yet it did grant for-profit businesses unprecedented religious rights and has inspired some large, ultraconservative religious organizations to demand still more freedom to discriminate. This means it is more important than ever that we work for clear, effective nondiscrimination laws.

That is why Out & Equal, Lambda Legal, and many other organizations have withdrawn support from the Senate-approved version of the Employment Non-Discrimination Act, which allows religious organizations — including hospitals, nursing homes, and many social services agencies — to discriminate based on sexual orientation and gender identity. Of course churches, other houses of worship, and religious schools must have full control over their selection of clergy and those who teach religion and lead religious activities. But when an organization invites people of all faiths (and no faith) to apply for jobs doing nonreligious work (such as food service, janitorial, medical, and business functions), those workers need to be treated just as fairly as in any work setting. No child labor or cheating on wages. No toxic chemicals in the air. And no toxic discrimination either.

Once upon a time, Southern restaurants used religion to explain racial segregation. Businesses have cited the Bible to justify paying women less than men. Attitudes about race and sex discrimination have evolved through a powerful mix of advocacy and outrage. This past spring, bills to allow religiously motivated anti-LGBT discrimination appeared in too many states, including Kansas, Georgia, and Arizona. Because community advocates, corporate leadership, and elected officials stood together, fairness prevailed. Now, given Hobby Lobby’s thumb on the scale for religious interests, it is ever more important that civic, business, and affirming faith leaders create an urgent chorus of support for explicit, effective and equal legal protections for LGBT people at every level of government. Our extraordinarily talented, diverse American community deserves no less.

JENNIFER C. PIZER is the law and policy project director for Lambda Legal.